Ultrafast structural molecular dynamics investigated with 2D infrared spectroscopy methods

Dynamics of Formamide-Water Mixtures Investigated by Linear and Nonlinear Infrared Spectroscopy

Formamide (FA) exhibits complete miscibility with water, offering a simplified model for exploring the solvation dynamics of peptide linkages in biophysical processes. Its liquid state demonstrates a three-dimensional hydrogen bonding network akin to water, reflecting solvent-like behavior. Analyzing the microscopic structure and dynamics of FA-water mixtures is expected to provide crucial insights into hydrogen bonding dynamics─a key aspect of various biophysical phenomena. This study is focused on the dynamics of FA-water mixtures using linear and femtosecond infrared spectroscopies. By using the intrinsic OD stretch and extrinsic probe SCN-, the local vibrational behaviors across various FA-water compositions were systematically investigated. The vibrational relaxation of OD stretch revealed a negligible impact of FA addition on the vibrational lifetime of water molecules, underscoring the mixture's water-like behavior. However, the reorientational dynamics of OD stretch slowed with increasing FA mole fraction (XFA), plateauing beyond XFA > 0.5. This suggests a correlation between OD's reorientational time and the strength of the hydrogen bond network, likely tied to the solution's changing dielectric constant. Conversely, the vibrational relaxation dynamics of SCN- was strongly correlated with XFA, highlighting a competition between water and FA molecules in solvating SCN-. Moreover, a linear relationship between rising viscosity and the prolonged correlation time of SCN-'s slow dynamics indicates that the solution's macroscopic viscosity is dictated by the extended structures formed between FA and water molecules. The relation between the reorientation dynamics of the SCN- and the macroscopic viscosity in aqueous FA-water mixture solutions was analyzed by using the Stokes-Einstein-Debye equations. The direct viscosity-diffusion coupling is observed, which can be attributed to the homogeneous dynamics feature in FA-water mixture solutions. The inclusion of these intrinsic and extrinsic probes not only enhances the comprehensiveness of our analysis but also provides valuable insights into various aspects of the dynamics within the FA-water system. This investigation sheds light on the fundamental dynamics of FA-water mixtures, emphasizing their molecular-level homogeneity in this binary mixture solution.

Biomolecular infrared spectroscopy: making time for dynamics

Time resolved infrared spectroscopy of biological molecules has provided a wealth of information relating to structural dynamics, conformational changes, solvation and intermolecular interactions. Challenges still exist however arising from the wide range of timescales over which biological processes occur, stretching from picoseconds to minutes or hours. Experimental methods are often limited by vibrational lifetimes of probe groups, which are typically on the order of picoseconds, while measuring an evolving system continuously over some 18 orders of magnitude in time presents a raft of technological hurdles. In this Perspective, a series of recent advances which allow biological molecules and processes to be studied over an increasing range of timescales, while maintaining ultrafast time resolution, will be reviewed, showing that the potential for real-time observation of biomolecular function draws ever closer, while offering a new set of challenges to be overcome.

Anion Recognition in Solution: Insights from Thermodynamics and Ultrafast Structural Dynamics

Anion recognition through noncovalent interactions stands as an emerging field in supramolecular chemistry, exerting a profound influence on the regulation of biological functions. Herein, the thermodynamics of complexation between sodium cyanate (NaOCN) and calix[4]pyrrole was systematically investigated by linear and nonlinear IR spectroscopy, highlighting enthalpy changes as the dominant driving force. The overall orientational relaxation of bound anion can be described by an Arrhenius-type activated process, yielding an activation energy of 15.0 ± 1.0 kJ mol-1. The structural dynamics of contact ion pairs (CIPs) formed between Na+ and OCN- in solution showed a negligible temperature effect, suggesting entropy changes as the principal governing factor. Further analysis revealed that anion recognition in solution is mediated by conformational changes of the receptor and collective rearrangement of hydrogen bond dynamics. This study, framed within the paradigms of thermodynamics and ultrafast structural dynamics, substantially advances our comprehension of the microscopic mechanisms underlying anion recognition in the realm of supramolecular chemistry.

Chain-like Structures Facilitate Li+ Transport in Concentrated Aqueous Electrolytes: Insights from Ultrafast Infrared Spectroscopy and Molecular Dynamics Simulations

Highly concentrated aqueous electrolytes have attracted attention due to their unique applications in lithium ion batteries (LIBs). However, the solvation structure and transport mechanism of Li+ cations at concentrated concentrations remain largely unexplored. To address this gap in knowledge, we employ ultrafast infrared spectroscopy and molecular dynamics (MD) simulations to reveal the dynamic and spatial structural heterogeneity in aqueous lithium chloride (LiCl) solutions. The coupling between the reorientation dynamics of the extrinsic probe and the macroscopic viscosity in aqueous LiCl solutions was analyzed using the Stokes-Einstein-Debye (SED) equations. MD simulations reveal that the Cl- and Li+ form chain-like structures through electrostatic interactions, supporting the vehicular migration of Li+ through the chain-like structure. The concentration dependent conductivity of the LiCl solution is well reproduced, where Li(H2O)2+ and Li(H2O)3+ are the dominant species that contribute to the conduction of Li+. This study is expected to establish correlations between ion pair structures and macroscopic properties.

Non-negligible Axial Ligand Effect on Electrocatalytic CO2 Reduction with Iron Porphyrin Complexes

Iron(III) porphyrin complexes have been demonstrated as one of the efficient molecular catalysts for the electrochemical reduction of CO₂. However, the role of axial ligands coordinated with a metal center in the complex on the electrochemical CO₂ reduction activity has not been fully explored yet. Herein, iron(III) tetraphenylporphyrin thiocyanate (FeTPP-SCN) is synthesized from a commercially available catalyst of FeTPP-Cl by a counteranion exchanging reaction. Cyclic voltammetry measurements showed that the catalytic activity of FeTPP-SCN is noticeably suppressed in the DMF solutions. The structural dynamics of the axial ligand in FeTPP-SCN are further examined by the FTIR and ultrafast IR spectroscopies, where the SCN ligand is employed as the local vibrational probe. Vibrational relaxation measurements showed that the reorientational dynamics of SCN ligands was strongly restricted in DMF solution, suggesting that the subtle electrostatic interaction between the ligands and metal center in the complex can have a non-negligible effect on its catalytic activity.

Distinct Hydrogen Bonding Dynamics Underlies the Microheterogeneity in DMF-Water Mixtures

The hydrogen bonding interaction between the amide functional group and water is fundamental to understanding the liquid-liquid heterogeneity in biological systems. Herein, the structure and dynamics of the N,N-dimethylformamide (DMF)-water mixtures have been investigated by linear and nonlinear IR spectroscopies, using the hydroxyl stretch and extrinsic probe of thiocyanate as local vibrational reporters. According to vibrational relaxation dynamics measurements, the orientational dynamics of water is not directly tied to those of DMF molecules. Wobbling-in-a-cone analysis demonstrates that the water molecules have varying degrees of angular restriction depending on their composition due to the formation of specific water-DMF networks. Because of the preferential solvation by DMF molecules, the rotational dynamics of the extrinsic probe is slowed significantly, and its rotational time constants are correlated to the change of solution viscosity. The unique structural dynamics observed in the DMF-water mixtures is expected to provide important insights into the underlying mechanism of microscopic heterogeneity in binary mixtures.

Structural Dynamics of Short Ligands on the Surface of ZnSe Semiconductor Nanocrystals

ZnSe semiconductor nanocrystals (NCs) with a size comparable to their Bohr radius are synthesized, and the native capping agents with long hydrocarbon tails are replaced with short thiocyanate (SCN) ligands through a ligand exchange method. The structural dynamics of SCN ligands on the surface of ZnSe NCs in solution is investigated by ultrafast infrared spectroscopy. Vibrational population relaxation of SCN ligands is accelerated due to the specific interaction with the positively charged sites on the surface of NCs. The orientational anisotropy of the bound SCN ligands decayed at a rate much faster than that in the control solution containing Zn²⁺ cations. From the wobbling-in-the-cone model analysis, we found that the SCN ligand undergoes wobbling orientational diffusion with a relatively large cone semiangle on the surface of ZnSe NCs, and the overall orientational diffusion of bound SCN is found to be strongly dependent on the size of ZnSe NCs.

Intermolecular Vibration Energy Transfer Process in Two CL-20-Based Cocrystals Theoretically Revealed by Two-Dimensional Infrared Spectra

Inspired by the recent cocrystallization and theory of energetic materials, we theoretically investigated the intermolecular vibrational energy transfer process and the non-covalent intermolecular interactions between explosive compounds. The intermolecular interactions between 2,4,6-trinitrotoluene (TNT) and 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) and between 1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX) and CL-20 were studied using calculated two-dimensional infrared (2D IR) spectra and the independent gradient model based on the Hirshfeld partition (IGMH) method, respectively. Based on the comparison of the theoretical infrared spectra and optimized geometries with experimental results, the theoretical models can effectively reproduce the experimental geometries. By analyzing cross-peaks in the 2D IR spectra of TNT/CL-20, the intermolecular vibrational energy transfer process between TNT and CL-20 was calculated, and the conclusion was made that the vibrational energy transfer process between CL-20 and TNTII (TNTIII) is relatively slower than between CL-20 and TNTI. As the vibration energy transfer is the bridge of the intermolecular interactions, the weak intermolecular interactions were visualized using the IGMH method, and the results demonstrate that the intermolecular non-covalent interactions of TNT/CL-20 include van der Waals (vdW) interactions and hydrogen bonds, while the intermolecular non-covalent interactions of HMX/CL-20 are mainly comprised of vdW interactions. Further, we determined that the intermolecular interaction can stabilize the trigger bond in TNT/CL-20 and HMX/CL-20 based on Mayer bond order density, and stronger intermolecular interactions generally indicate lower impact sensitivity of energetic materials. We believe that the results obtained in this work are important for a better understanding of the cocrystal mechanism and its application in the field of energetic materials.

Revealing the Relationship between Electric Fields and the Conformation of Oxytocin Using Quasi-Static Amide-I Two-Dimensional Infrared Spectra

It is reported that the cis/trans conformation change of the peptide hormone oxytocin plays an important role in its receptors and activation and the cis conformation does not lead to antagonistic activity. Motivated by recent experiments and theories, the quasi-static amide-I 2D IR spectra of oxytocin are investigated using DFT/B3LYP (D3)/6-31G (d, p) in combination with the isotope labeling method under different electric fields. The theoretical amide-I IR spectra and bond length of the disulfide bond are consistent with the experimental values, which indicates that the theoretical modes are reasonable. Our theoretical results demonstrate that the oxytocin conformation is transformed from the cis conformation to the trans conformation with the change of the direction of the electric field, which is confirmed by the distance of the backbone carbonyl oxygen of Cys6 and Pro7, the Ramachandran plot of Cys6 and Pro7, the dihedral angle of C_β-S-S-C_β, and the rmsd of the oxytocin backbone. Moreover, the trans conformation as the result of the turn in the vicinity of Pro7 has a tighter secondary spatial structure than the cis conformation, including stronger hydrogen bonds, longer γ-turn geometry involving five amino acids, and a more stable disulfide bond. Our work provides new insights into the relationship between the conformation, the activation of the peptide hormone oxytocin, and the electric fields.

Exploring the Structure and Complexation Dynamics of Azide Anion Recognition by Calix[4]pyrroles in Solution

The structure and anion recognition dynamics between calix[4]pyrroles and azide (N₃^-) anions in the form of its TBA⁺ and Na⁺ salts were investigated in dimethyl sulfoxide solutions by Fourier transform infrared (FTIR) spectroscopy and ultrafast IR spectroscopy. Vibrational energy redistribution of the N₃^- anion in the complex is accelerated through hydrogen bonding interactions with the N-H proton of the receptor. Rotational dynamics of the bound N₃^- is greatly restricted, demonstrating a distinct countercation effect. The detailed binding modes of N₃^- with the receptor were further evaluated by the density functional theoretical (DFT) calculations and nuclear magnetic resonance (NMR) spectroscopy. All of these measurements support the notion that the calix[4]pyrroles are capable of capturing the azide anion in solution. However, the calix[4]pyrroles may not necessarily undergo a conformational change to a cone-like geometry when they bind to the azide anion in the solution.

Direct observation of reversible bond homolysis by 2D EXSY NMR

Bond homolysis is one of the most fundamental bond cleavage mechanisms. Thus, understanding of bond homolysis influences the development of a wide range of chemistry. Photolytic bond homolysis and its reverse process have been observed directly using time-resolved spectroscopy. However, direct observation of reversible bond homolysis remains elusive. Here, we report the direct observation of reversible Co–Co bond homolysis using two-dimensional nuclear magnetic resonance exchange spectroscopy (2D EXSY NMR). The characterization of species involved in this homolysis is firmly supported by diffusion ordered NMR spectroscopy (DOSY NMR). The unambiguous characterization of the Co–Co bond homolysis process enabled us to study ligand steric and electronic factors that influence the strength of the Co–Co bond. Understanding of these factors will contribute to rational design of multimetallic complexes with desired physical properties or catalytic activity.

We report the first direct observation of reversible bond homolysis using EXSY NMR. This study revealed that electron donating groups weaken the Co–Co bond.

Cationic Effects on the Structural Dynamics of the Metal Ion-Crown Ether Complexes Investigated by Ultrafast Infrared Spectroscopy

It is usually believed that the binding affinity and selectivity of an alkali metal ion with crown ether are defined by the size matching model. However, the underlying mechanism of the specific host-guest interactions and the structural dynamics of the metal ions confined in the cavity of the crown ethers in the solutions are still not clear. In this report, a series of alkali thiocyanate salts (XSCN; X = Li, Na, K, and Cs) complexed with 18-crown-6 (a typical crown ether) in the chloroform solutions were studied by the polarization-selective infrared pump-probe spectroscopy and the ultrafast two-dimensional infrared (2D IR) spectroscopy. The SCN^- counteranions were employed as the local vibrational probe to reveal the specific host-guest interactions in the crown ether complexes. The rotational dynamics and spectral diffusion of SCN^- vibration were both measured by ultrafast IR spectroscopy, and it was found that the metal cations hosted by the crown ethers can have a pronounced effect on the rotational dynamics of the counteranions. The reorientational time constants of the SCN^- vibration in the complexation follow the order Li⁺ > Na⁺ > K⁺ ≃ Cs⁺. More importantly, the spectral diffusion dynamics of SCN^-, which quantifies the decay of the correlation of the frequency fluctuations in the complexation, was also affected by the metal ions but showed a different order of cationic effect. A detailed analysis of the 2D IR data showed that the spectral diffusion of SCN^- counteranion clearly decayed with two different time scales in the complex of 18-crown-6 with K⁺. The 3-4-fold slowdown in spectral diffusion indicated that the fluctuation of SCN^- vibrational transition frequency was strongly affected by the K⁺ cation due to the geometric constraint imposed by the crown ether. The results should help the researchers to unravel the specific host-guest interactions and further reveal the origination of the binding selectivity of crown ether for metal cations in the condensed phases from the perspective of structural dynamics.

Two-dimensional Infrared Spectroscopy Reveals Better Insights of Structure and Dynamics of Protein

Proteins play an important role in biological and biochemical processes taking place in the living system. To uncover these fundamental processes of the living system, it is an absolutely necessary task to understand the structure and dynamics of the protein. Vibrational spectroscopy is an established tool to explore protein structure and dynamics. In particular, two-dimensional infrared (2DIR) spectroscopy has already proven its versatility to explore the protein structure and its ultrafast dynamics, and it has essentially unprecedented time resolutions to observe the vibrational dynamics of the protein. Providing several examples from our theoretical and experimental efforts, it is established here that two-dimensional vibrational spectroscopy provides exceptionally more information than one-dimensional vibrational spectroscopy. The structural information of the protein is encoded in the position, shape, and strength of the peak in 2DIR spectra. The time evolution of the 2DIR spectra allows for the visualisation of molecular motions.

Quasi-Static Two-Dimensional Infrared Spectra of the Carboxyhemoglobin Subsystem under Electric Fields: A Theoretical Study

There is no doubt that electric fields of a specific frequency and intensity could excite certain vibrational modes of a macromolecule, which alters its mode coupling and conformation. Motivated by recent experiments and theories, we study the mode coupling between the Fe-CO mode and CO-stretch mode and vibration energy transfer among the active site and proteins in carboxyhemoglobin (HbCO) under different electric fields using the quasi-static two-dimensional infrared spectra. This study uses iron-porphyrin-imidazole-CO and two distal histidines in HbCO as the subsystem. The potential energy and dipole moment surfaces of the subsystem are calculated using an all-electron ab initio (B3LYP-D3(BJ)) method with the basis set Lanl2dz for the Fe atom and 6-31G(d,p) for C, H, O, and N atoms. Although the subsystem is reduced dimensionally, the anharmonic frequency and anharmonicity of the CO-stretch mode show excellent agreement with experimental values. We use the revealing noncovalent interaction method to confirm the hydrogen bond between the H_ε atom of the His63 and the CO molecule. Our study confirms that the mode coupling between the Fe-CO mode and CO-stretch mode does not exist when the subsystem is free of electric field perturbation, which is coupled when the electric field is -0.5142 V/nm. In addition, with the increases of distance between the active site and the His92, there is no vibrational energy transfer between them when the electric field is 1.028 V/nm. We believe that our work could provide new ideas for increasing the dissociation efficiency of the Fe-CO bond and theoretical references for experimental research.

Specific Host-Guest Interactions in the Crown Ether Complexes with K+ and NH4+ Revealed from the Vibrational Relaxation Dynamics of the Counteranion

The specific host-guest interactions in the corresponding complexes of K⁺ and NH₄⁺ with typical crown ethers were investigated by using FTIR and ultrafast IR spectroscopies. The counteranions, i.e., SCN^-, were employed as a local vibrational probe to report the structural dynamics of the complexation. It was found that the vibrational relaxation dynamics of the SCN^- was strongly affected by the cations confined in the cavities of the crown ethers. The time constant of the vibrational population decay of SCN^- in the complex of NH₄⁺ with the 18-crown-6 was determined to be 6 ± 2 ps, which is ∼30 times faster than that in the complex of K⁺ with the crown ethers. Control experiments showed that the vibrational population decay of SCN^- depended on the size of the cavities of the crown ethers. A theoretical calculation further indicated that the nitrogen atom of SCN^- showed preferential coordination to the K⁺ ions hosted by the crown ethers, while the NH₄⁺ can form hydrogen bonds with the oxygen atoms in the studied crown ethers. The geometric constraints formed in the complex of crown ethers can cause a specific interaction between the NH₄⁺ and SCN^-, which can facilitate the intermolecular vibrational energy redistribution of the SCN^-.

Proving and Probing the Presence of the Elusive C-H⋅⋅⋅O Hydrogen Bond in Liquid Solutions at Room Temperature

Hydrogen bonds (H bonds) play a major role in defining the structure and properties of many substances, as well as phenomena and processes. Traditional H bonds are ubiquitous in nature, yet the demonstration of weak H bonds that occur between a highly polarized C-H group and an electron-rich oxygen atom, has proven elusive. Detailed here are linear and nonlinear IR spectroscopy experiments that reveal the presence of H bonds between the chloroform C-H group and an amide carbonyl oxygen atom in solution at room temperature. Evidence is provided for an amide solvation shell featuring two clearly distinguishable chloroform arrangements that undergo chemical exchange with a time scale of about 2 ps. Furthermore, the enthalpy of breaking the hydrogen bond is found to be 6-20 kJ mol^-1 . Ab-initio computations support the findings of two distinct solvation shells formed by three chloroform molecules, where one thermally undergoes hydrogen-bond making and breaking.

Ultrafast vibrational coupling between C H and C O band of cyclic amide 2-Pyrrolidinone revealed by 2DIR spectroscopy

Coupling between C H and C O vibrational modes play an essential role on determination of biological structure and dynamics. However, due to the weakness of the C H absorption and strong absorption of the C O vibrational band make such experiments less straightforward than those with transitions of nearly the same strength. In this communication the characteristics of the C H and C O coupling has been studied using dual frequency two dimensional infrared spectroscopy. 2-Pyrrolidinone has been used as a model molecule of biological system. The coherent and incoherent couplings between C H and C O vibrational bands have been observed. The cross peaks dynamics have been discussed and time constant of the cross peak intensity has been calculated.

Vibrational Relaxation Dynamics of a Semiconductor Copper(I) Thiocyanate (CuSCN) Film as a Hole-Transporting Layer

The semiconductor CuSCN film, which is typically used as the hole-transporting layer (HTL) in solar cell studies, has been investigated by Fourier transform infrared (FTIR) spectroscopy and ultrafast transient infrared (IR) spectroscopy. A sharp peak at 2175 cm^-1 corresponding to the CN vibrational stretching mode in CuSCN was observed, and the peak frequency remained unchanged by varying the thickness of the CuSCN thin film. Vibrational relaxation measurements showed that the 0-1 and 1-2 transitions of CN stretching can be observed at 2175 and 2140 cm^-1, respectively. The heat-induced absorption and bleaching peaks (2167 and 2175 cm^-1) can be clearly seen at a waiting time of 40 ps. The vibrational relaxation of the CN stretching mode determined from the 1-2 transition exhibited a biexponential decay with time constants of 7.4 ± 0.5 (90%) and 158 ± 50 ps (10%). Importantly, the abnormal anisotropy decay of the CN stretching mode in the CuSCN thin film was also observed for the first time. A detailed analysis showed that the distinct anisotropy decay curve could be described using a triexponential decay function, which was explained by three different processes: resonance energy transfer (∼8 ps), a thermalization process (∼40 ps), and molecular rotation (∼150 ps). The time scale of the thermalization process caused by the vibrational relaxation in CuSCN is at a time scale of 40 ps, which is important for us to understand the thermally activated charge-transport property of the CuSCN film employed as the HTL. Further UV pump-IR probe measurement revealed that the carrier scattering and relaxation processes in the CuSCN film are strongly associated with the vibrational excitation and relaxation dynamics of the CN stretching mode. It is expected that the fundamental understanding of the vibrational relaxation dynamics of the CuSCN thin film should provide helpful insight to elucidate its role as the HTL in solar cell studies at the molecular level.

Note: An automatic liquid nitrogen refilling system for small (detector) Dewar vessels

Many infrared spectroscopy setups are in principle stable enough to run overnight or longer, but the detector's Dewar vessel must be refilled manually with liquid nitrogen (LN₂) every couple of hours. Commercial automatic LN₂ refilling systems work reliably only for large Dewars. Here, we present a refilling system which can non-invasively be applied to already installed small Dewars. The system reliably refills LN₂ once it has dropped below an adjustable level, with quick refilling (<3 min) for a 0.6 l Dewar. Our design protects the setup and the detector from overflowing or running without LN₂.

Controlling Photochemistry via Isotopomers and IR Pre-excitation

It is a photochemist's dream to be able to photoinduce a reaction of a specific molecular species in an ensemble of similar but not identical ones. The problem is that similar molecules often exhibit nearly identical UV-Vis absorption spectra, making them difficult or impossible to distinguish or to select spectroscopically. The ultrafast VIPER (VIbrationally Promoted Electronic Resonance) pulse sequence allows to pick a single species for electronic excitation based on its infrared spectrum. The latter usually shows more features, allowing the discrimination between species than the UV-Vis spectrum. Here, we show that it is possible to induce and monitor species-selective photochemistry even for molecules with virtually identical UV-Vis spectra, which is the case for isotopomers. Next to isotope-selective photochemistry in solution, applications to orthogonal photo-uncaging and species-selective spectroscopy and photochemistry in mixtures are within reach.

Plasmonic Substrates Do Not Promote Vibrational Energy Transfer at Solid-Liquid Interfaces

Intermolecular vibrational energy transfer in monolayers of isotopically mixed rhenium carbonyl complexes at solid-liquid interfaces is investigated with the help of ultrafast 2D Attenuated Total Reflectance Infrared (2D ATR IR) spectroscopy in dependence of plasmonic surface enhancement effects. Dielectric and plasmonic materials are used to demonstrate that plasmonic effects have no impact on the vibrational energy transfer rate in a regime of moderate IR surface enhancement (enhancement factors up to ca. 30). This result can be explained with the common image-dipole picture. The vibrational energy transfer rate thus can be used as a direct observable to determine intermolecular distances on surfaces, regardless of their plasmonic properties.